So, what have you done in the meantime? What else do you have running? Who is hogging the CPU? That's almost always the cause of choppy video, especially when you have a local copy cached. htop and atop are your friends.
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Andrew BealsJun 22 '12 at 20:37

I have an i7 and a NVS 4200m, no one is hogging the CPU. I am running Blender, but that's Python and its single threaded. I am not doing any rendering. This is a problem in the OS/drivers/settings.
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ConstantinJun 22 '12 at 20:50

I'm running the same flash plugin and on a Core2, which is much slower than your box, yet I'm not having any problems. How old is your system drive? The original HDD in my system started slowing down and giving choppy access which blew performance out of the water - replaced it and everything's much better now.
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Andrew BealsJun 22 '12 at 21:06

I specifically pointed out atop because it will show process exits which can kill your performance without otherwise registering activity.
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Andrew BealsJun 22 '12 at 21:07

Hi Andrew, I would like to reiterate, this is not a hardware issue. The closest related hardware issue is the Optimus technology my laptop runs, but that is disabled... The problem lies in 12.04. I was running 10.04 perfectly a few days ago ... I don't know why I upgraded, I wish I hadn't.
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ConstantinJun 22 '12 at 21:10

remove the flash plugin installed by firefox itself, install the one from the repository (apt-get install adobe-flashplugin). The problem changed (instead of slow and choppy it was now too fast and only clicks for audio).

try to use gnash instead, but the gnash packages in the repository seem to not install a firefox plugin at all.

switch youtube to html5, but the video I wanted wasn't available in WebM, and installing x264 and chromium didn't help either

In the end, I used the DownloadHelper addon to simply download the video (but that is of course a VERY ugly solution for only a few use cases.

Also... cranking up the sound quality settings in pulse audio might also help:

sudo nano /etc/pulse/daemon.conf

Scroll down where it says default-sample-rate and change it to 48000 (dont forget to remove the semi-colon !! )
Also if you have a relatively good cpu you can improve the audio quality a little more by moving a few lines up, to the "resample-method" line and change the speex-float number to 5 .
Ctrl+o and ctrl+x to save and exit. Restart pulse audio or the whole system for the settings to kick in.

Disable hardware acceleration by right clicking in flashplayer window >settings>un-check hardware acc. I had terrible playback and frequent crashing in both chrome and firefox. Was impossible to watch anything. Simply right clicking and on the flash player and disabling hardware acc. FIXED jerkiness right away. Now seems playback smoothness depends on CPU load.
TRY FIRST!!
Less crashing already.